Amoeboid designs complex transportation network, eats oats

Research conducted with a simple slime mold shows that it can grow complex …

For anyone interested in going into engineering, I can offer a warning: prepare to get your butt handed to you repeatedly by nature. Many of the processes at the forefront of engineering technology are just trying to play catch-up with what nature has done an innumerable number of times. Photosynthesis, genetic replication, the creation of joints, even the simple act of flight—nature has done it before, with greater ease, and often cheaper or more efficiently.

A paper in the current issue of Science discusses the ability of a single-celled creature to create a robust network while foraging for food—one that mimicked the Tokyo rail system in complexity. Creating a good network is a balancing act; you need to span a large number of nodes with a minimal number of edges (keeping cost low), while being able to function when an edge is lost (fault tolerant). Problems of this type are a shining example of the adage "fast, cheap, or good: pick any two."

Many organisms grow in the form of a connected network, and they have the benefit of innumerable generations of natural selection behind them. Selective pressures have forced the organism to find a happy balance among connectedness, fault tolerance, and cost/efficiency. The authors of the Science article use the slime mold Physarum polycephalum as their biological network generator, and it served as a muse for the creation of an adaptive network model.

Physarum is a single-celled amoeboid organism that spends its time searching for physically distributed sources of food. When starting on a fresh substrate, it spreads in all directions to maximize the area it is capable of searching. Behind the outer perimeter of its search area, it forms a tubular network that connects cells to any food sources that it has discovered. Over the course of a few hours, the network it forms connects the food sources in a manner that optimizes the network's properties.

As part of their experimentation with the slime, the researchers placed 36 food sources on a substrate in a manner that mimicked the geographical layout of cities around Tokyo. (Physarum is apparently fond of oat flakes.) They then introduced the slime mold to the foraging grounds and compared the network that it formed with the actual Tokyo rail network in place around the city.

Initially, the Physarum began to spread out over the entire available area but, over time, it concentrated its network on the tubes that connected the food sources. The resulting network topology "bore similarity to the real rail network." To see if the organism could be coaxed into an even closer match, the researchers used light—which is known to inhibit the growth of physarum—to simulate mountains, lakes, or similar impasses that the actual rail network must contend with.

While looking like the real network is nice, it's not exactly an objective measure. To attempt to quantify the similarity, the researchers examined a handful of metrics used for describing topological networks. The cost of the network (total length), efficiency (average minimum distance between nodes), and robustness (degree of fault tolerance) were examined relative to the minimum spanning tree (MST) for each network. The MST represents the smallest possible network that connects all the food source (or city rail station) positions.

When compared to the length of the MST, the Tokyo rail system was 1.8 times larger, while the Physarum network was 1.75�0.30 times larger. The average minimum distance between cities (food sources) was 0.85 and 0.85�0.04, respectively. These two measurements illustrate the fact that Physarum-based networks have a lower "cost" but provide a relatively equal distance between nodes.

One place where engineers did a bit better: the amoeba's networks were not as robust as the actual rail network. For the rails, four percent of the possible faults could lead to the isolation of a node, whereas a fault in the Physarum network has a 14�4 percent chance of leading to an isolated food source. That just won't do for Tokyo, given the frequency of monster attacks there.

Using these observations of network formation, the researchers attempted to develop a model that was capable of describing the network's formation. Using a simple fluid flow model for the arms, along with sink/source terms to represent the food sources, they were able to reproduce the Physarum network with the help of a pair of free parameters. The authors conclude that planners might consider using the model during the preliminary planning stages of other self-organized networks, such as remote sensors arrays or mobile, ad-hoc networks.

Nature doesn't always "engineer" the most optimal solution to a problem.....in many cases, it's on its' way to finding the most optimal route, but hasn't gotten there yet. Or at some point in evolution "realized" that the current solution was "good enough".

Nature has good solutions to engineering problems, but not always the best.

Originally posted by Ninhalem:Could that organism replace engineers by laying out the network for rail systems ahead of time for a specific city and then just build according to the layout it produced?

That would be pretty cool, an organic, sentient, self-optimizing rail system. Our mass-transit system in California is busted and rife with corrupt officials and competing agencies, I would gladly welcome our new amoeba overlords to replace the current slime (molds).

The authors conclude that planners might consider using the model during the preliminary planning stages of other self-organized networks, such as remote sensors arrays or mobile, ad-hoc networks.

Now *that* is a cool idea. As for those worrying about being amoeba-sourced, someone still has to program the light displays to simulate obstructions and actually build the damn thing. And, of course, decide if the amoeba built an optimum network.

When compared to the length of the MST, the Tokyo rail system was 1.8 times larger, while the Physarum network was 1.75±0.30 times larger. The average minimum distance between cities (food sources) was 0.85 and 0.85±0.04, respectively. These two measurements illustrate the fact that Physarum-based networks have a lower "cost" but provide a relatively equal distance between nodes.

Doesn't this mean that the actual MST comparison value can only be said to within the range of 1.45 - 2.05? Since the rail system's value falls pretty close to the median of that range how can you reach this conclusion with any confidence? Same thing with the other one too. Please correct me if I'm being stupid.

The authors conclude that planners might consider using the model during the preliminary planning stages of other self-organized networks, such as remote sensors arrays or mobile, ad-hoc networks.

Now *that* is a cool idea. As for those worrying about being amoeba-sourced, someone still has to program the light displays to simulate obstructions and actually build the damn thing. And, of course, decide if the amoeba built an optimum network.

No actual amoebas needed. They have developed a mathematical model which simulates the amoeba.

Nature has good solutions to engineering problems, but not always the best.

Agree. Even the fundamental Krebs energy cycle of cells could stand to be tweaked. Of course, you have to give humans credit. It's taken nature millions of years to create its stuff. We've only been around for 500-100k years (depending on what you count as "human", which is itself an argument), and look at how far we've gotten. Of course, a lot of what we've done has been to *cough* copy nature, but, you know, it's not really "copying", it's "paying homage to", and it's not like nature was smart enough to patent its ideas anyways.

A paper in the current issue of Science discusses the ability of a single-celled creature to create a robust network while foraging for food—one that mimicked the Tokyo rail system in complexity.

DESIGNER! DEEEEEEESIIIIIIIIIIIIIIIIGNER!!!

quote:

Many organisms grow in the form of a connected network, and they have the benefit of innumerable generations of natural selection behind them. Selective pressures have forced the organism to find a happy balance among connectedness, fault tolerance, and cost/efficiency.

"For anyone interested in going into engineering, I can offer a warning: prepare to get your butt handed to you repeatedly by nature."

Trying being a chemical engineer. They have it the worse in this respect.

Production of ammonia? Destroyed by nature. Reduction of CO2 to hydrocarbons. Destroyed by nature. Production of light, ultrastrong material (eg. bone, tendon, etc.) destroyed by nature. Ability to produce intense nanoscale machines. Destroyed by nature. Ability to store information in a chemical form? Destroyed by nature. The list goes on and on...

Photosynthesis, genetic replication, the creation of joints, even the simple act of flight—nature has done it before, with greater ease, and often cheaper or more efficiently.

To be fair, life forms spend many long years and uncounted dead ancestors to arrive at the solutions you find in nature, so I'm not sure easy and efficient are the best words. The old saw about monkeys and typewriters comes to mind.

quote:

The authors conclude that planners might consider using the model during the preliminary planning stages of other self-organized networks, such as remote sensors arrays or mobile, ad-hoc networks.

I think this would have pretty cool applications in vehicle routing systems for multiple destinations, or for delivery software.

In all seriousness though, I'd love to see this model applied to FPGA signal routing where the current approach seems to consist of randomly mixing things up until they happen to work within the constraints. Doesn't solve placement though... maybe if we fed the amoeboid wheat germ instead of oat flakes?

When compared to the length of the MST, the Tokyo rail system was 1.8 times larger, while the Physarum network was 1.75±0.30 times larger. The average minimum distance between cities (food sources) was 0.85 and 0.85±0.04, respectively. These two measurements illustrate the fact that Physarum-based networks have a lower "cost" but provide a relatively equal distance between nodes.

Doesn't this mean that the actual MST comparison value can only be said to within the range of 1.45 - 2.05? Since the rail system's value falls pretty close to the median of that range how can you reach this conclusion with any confidence? Same thing with the other one too. Please correct me if I'm being stupid.

I agree, assuming these values are the average of many repeated experiments it appears from the mean/stdev that the values are unlikely to be different at a statistically significant level.

Originally posted by RockDaMan:"For anyone interested in going into engineering, I can offer a warning: prepare to get your butt handed to you repeatedly by...the Creator"

There, fixed that for you.

No, you haven't. You've just turned the topic from something entirely uncontroversial to something that now has a religious component, which is needlessly distracting. Additionally, your "fix" was completely unnecessary anyway, given that the word, "nature", does not deny the existence of a creator for those who believe in that kind of thing.

In other words, STFU and stop injecting your personal bullshit where it doesn't belong.

Doh! Transit planning epic fail! OK, this is really cool, and has all sorts of applications, but this system exhibits the single biggest screwup in transit system planning: it is a network that links destinations, rather than serving the trips that passengers actually want to make.

It's much, much easier to link a bunch of destinations, and doing so is better than nothing. But a well designed transit system looks at where trips begin and end, and then designs the system to serve the actual trips that passengers want to make. Start thinking about that task, and you'll realize just how much more difficult that task actually is. In the Tokyo metro area, many, many people want to travel from the surrounding residential centers into and out of the core Tokyo area, so the network you see above is pretty good. (Actually, the core of Tokyo is several distinct sub-centers, but that's splitting hairs.) In comparison, planning a transit network for any of the major American metro areas is much more difficult. In the past, suburbanites lived in bedroom communities and commuted into the city center. Today, people live in one burb and work far away in another burb, and many live in the city center and work out in the burbs. This requires a transit network that is quite different than the network you see the slime forming above.

(Also, at the core of this story is the assumption that the human-designed rail network was anything like optimal. It might actually be so, but the history of the development of rail networks in major metro areas is very complicated with travel patterns, transport technology and legal issues changing significantly over time, and each new revision to the system having to be built on the pre-existing network, rather than being able to design from scratch. Also, the transportation network itself drives where development occurs, so in this case, the oats would move around depending on where the slime is...)

I often hear this but I think people who say it don't quite grasp the sheer volume and rate of evolutionary changes in micro-organisms. In 100 ml of sea water there might be 10 billion single celled organisms including prokaryots, eukaryots, plants, animals, fungi etc. etc. (plus virsus, and that's another whole evolutionary conundrum).

Now some of these single celled organisms might have 4 hour generations times. So picture 10 billion organisms turning over 6 generations a day.

Now the ocean has thousands of cubic kilometres of space and this experiment has been running for billions of years. Just stop for a minute, and imagine the sheer scale of that. It makes my brain melt every time.

quote:Originally posted by RockDaMan:"For anyone interested in going into engineering, I can offer a warning: prepare to get your butt handed to you repeatedly by...the Creator"

There, fixed that for you.

No, you haven't. You've just turned the topic from something entirely uncontroversial to something that now has a religious component, which is needlessly distracting. Additionally, your "fix" was completely unnecessary anyway, given that the word, "nature", does not deny the existence of a creator for those who believe in that kind of thing.

In other words, STFU and stop injecting your personal bullshit where it doesn't belong.

Matt Ford / Matt is a contributing writer at Ars Technica, focusing on physics, astronomy, chemistry, mathematics, and engineering. When he's not writing, he works on realtime models of large-scale engineering systems.